Miller claims that the problem with anti-evolutionists like Michael Behe and me is a failure of imagination -- that we personally cannot "imagine how evolutionary mechanisms might have produced a certain species, organ, or structure." He then emphasizes that such claims are "personal," merely pointing up the limitations of those who make them. Let's get real. The problem is not that we in the intelligent design community, whom Miller incorrectly calls "anti-evolutionists," just can't imagine how those systems arose. The problem is that Ken Miller and the entire biological community haven't figured out how those systems arose. It's not a question of personal incredulity but of global disciplinary failure (the discipline here being biology) and gross theoretical inadequacy (the theory here being Darwin's).

However, with confronted with rather a lot of literature on the origin and evolution of the immune system (one of Behe's originally identified IC systems from Darwin's Black Box, plus lots of evidence of precursors in organisms without the full system, not a single IDist was able to defend the previous statements of Behe and Dembski along the lines of "the entire biological community ha[s]n't figured out how those systems arose." A few of the more sophisticated ID-friendlies even appeared to agree that the gradual evolution of the "IC" immune system was a perfectly reasonable idea supported by a fair number of observations and peer-reviewed articles.

And yes, this will keep getting brought up as long as Dembski keeps repeating the same false line that biologists are clueless about how complex multipart systems can originate.

As for what things like the Type III secretion system do and do not prove (as well as for citations of important bits of evidence that Dembski failed to deal with, things like the Exb homologs of the flagellum motor proteins, and the archaeal flagellum--Type IV secretion system homologies), there's not much point in repeating them yet again, so I've been accumulating a list of the relevant links here: